Hi I've gone from Wendouree to Southern Cross Station many times and the train is never overflowing I always go with the very comfortable velocity V line and get there in about just over an hour very relaxing smooth ride easy to get to Melbourne and back.
Yes... and No... It all depends what time you travel and what you are used to. Many people do the commute quite happily and dont have any problems other than the odd train delay. Earlier trains tend to run a better service and getting out of Melbourne in the afternoon peak hour can be quite busy. The Ballarat line upgrades have commenced which will result in loads more trains and a quicker more reliable service. You could easily have a far more painful commute living in the Melbourne suburbs.